administering pathway tools
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Administering Pathway Tools. Obtaining Pathway Tools. Free to non-commercial organizations To obtain license agreement go to BioCyc.org and click on Software/Database Download Follow Installation Guide ptools-local directory Locate in common directory

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obtaining pathway tools
Obtaining Pathway Tools
  • Free to non-commercial organizations
  • To obtain license agreement go to BioCyc.org and click on Software/Database Download
  • Follow Installation Guide
  • ptools-local directory
    • Locate in common directory
    • PGDBs created by all users who use this ptools installation
    • PGDBs downloaded via the registry
    • ptools-init.dat for this ptools installation
new pathway tools releases
New Pathway Tools Releases
  • Major releases = External software releases
    • Twice per year
    • Announced on ptools-users mailing list
  • Minor releases twice per year affect only our BioCyc.org Web site and flatfile distributions
  • We support one prior release only
  • Releases announced on [email protected]
  • Read release notes at
    • http://brg.ai.sri.com/ptools/release-notes.html
  • Install process:
    • Upgrade schema of your DB (software assisted)
pgdb storage file or relational database
PGDB Storage:File or Relational Database
  • File storage:
    • Advantages:
      • No RDBMS installation and configuration
    • Disadvantages:
      • Must be loaded and saved in its entirety
      • No transaction history
      • No concurrent access for multiple users
  • Oracle/MySQL storage:
    • Advantages:
      • Faster read access, faster saves
      • Concurrent update access for multiple users
      • Stores history of all PGDB updates
    • Disadvantages:
      • RDBMS must be installed and configured
multiuser access to pgdbs
Multiuser Access to PGDBs
  • PGDB stored within one Oracle or MySQL server
  • Each curator installs PTools on their workstation
  • Different curators can use different software platforms
  • Workstations query RDBMS server via internet
  • Local disk cache speeds access
  • For each frame access, PTools queries
    • In-memory cache, disk cache, RDBMS server
  • After curator saves changes, all changes made by other users are loaded into curator’s session
how to release a pgdb
How to Release a PGDB?
  • Decide on release frequency and schedule
    • Don’t wait until it’s perfect to release it!
  • Freeze curation for 1 week
  • Quality assurrance
    • Run consistency checker
      • Tools -> Consistency Checker
      • Also updates organism-summary statistics
  • Update publications, authors in organism frame
    • Update via Organism editor
  • Create new version of PGDB
    • ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelot
    • Edit against the new version, release the old version
  • Author release notes
  • Register PGDB in SRI PGDB registry
    • Will allow SRI to include it in BioCyc
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